Skip to content

Commit 5497960

Browse files
pinin4fjordspinin4fjords
committed
Fix orderings
1 parent 9f1c33f commit 5497960

14 files changed

+31
-31
lines changed

‎tests/default.nf.test.snap‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1219,16 +1219,16 @@
12191219
"star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls",
12201220
"star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls",
12211221
"star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls",
1222+
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
12221223
"star_salmon/salmon.merged.gene_counts.tsv",
12231224
"star_salmon/salmon.merged.gene_counts_length_scaled.tsv",
12241225
"star_salmon/salmon.merged.gene_counts_scaled.tsv",
12251226
"star_salmon/salmon.merged.gene_lengths.tsv",
12261227
"star_salmon/salmon.merged.gene_tpm.tsv",
1228+
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
12271229
"star_salmon/salmon.merged.transcript_counts.tsv",
12281230
"star_salmon/salmon.merged.transcript_lengths.tsv",
12291231
"star_salmon/salmon.merged.transcript_tpm.tsv",
1230-
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
1231-
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
12321232
"star_salmon/samtools_stats",
12331233
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
12341234
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",

‎tests/featurecounts_group_type.nf.test.snap‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1185,16 +1185,16 @@
11851185
"star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls",
11861186
"star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls",
11871187
"star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls",
1188+
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
11881189
"star_salmon/salmon.merged.gene_counts.tsv",
11891190
"star_salmon/salmon.merged.gene_counts_length_scaled.tsv",
11901191
"star_salmon/salmon.merged.gene_counts_scaled.tsv",
11911192
"star_salmon/salmon.merged.gene_lengths.tsv",
11921193
"star_salmon/salmon.merged.gene_tpm.tsv",
1194+
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
11931195
"star_salmon/salmon.merged.transcript_counts.tsv",
11941196
"star_salmon/salmon.merged.transcript_lengths.tsv",
11951197
"star_salmon/salmon.merged.transcript_tpm.tsv",
1196-
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
1197-
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
11981198
"star_salmon/samtools_stats",
11991199
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
12001200
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",

‎tests/hisat2.nf.test.snap‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1161,8 +1161,6 @@
11611161
"salmon/WT_REP2/logs/salmon_quant.log",
11621162
"salmon/WT_REP2/quant.genes.sf",
11631163
"salmon/WT_REP2/quant.sf",
1164-
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
1165-
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
11661164
"salmon/deseq2_qc",
11671165
"salmon/deseq2_qc/R_sessionInfo.log",
11681166
"salmon/deseq2_qc/deseq2.dds.RData",
@@ -1176,11 +1174,13 @@
11761174
"salmon/deseq2_qc/size_factors/WT_REP1.txt",
11771175
"salmon/deseq2_qc/size_factors/WT_REP2.txt",
11781176
"salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
1177+
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
11791178
"salmon/salmon.merged.gene_counts.tsv",
11801179
"salmon/salmon.merged.gene_counts_length_scaled.tsv",
11811180
"salmon/salmon.merged.gene_counts_scaled.tsv",
11821181
"salmon/salmon.merged.gene_lengths.tsv",
11831182
"salmon/salmon.merged.gene_tpm.tsv",
1183+
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
11841184
"salmon/salmon.merged.transcript_counts.tsv",
11851185
"salmon/salmon.merged.transcript_lengths.tsv",
11861186
"salmon/salmon.merged.transcript_tpm.tsv",

‎tests/kallisto.nf.test.snap‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -138,12 +138,12 @@
138138
"kallisto/WT_REP2/kallisto_quant.log",
139139
"kallisto/WT_REP2/run_info.json",
140140
"kallisto/kallisto.merged.gene.SummarizedExperiment.rds",
141-
"kallisto/kallisto.merged.transcript.SummarizedExperiment.rds",
142141
"kallisto/kallisto.merged.gene_counts.tsv",
143142
"kallisto/kallisto.merged.gene_counts_length_scaled.tsv",
144143
"kallisto/kallisto.merged.gene_counts_scaled.tsv",
145144
"kallisto/kallisto.merged.gene_lengths.tsv",
146145
"kallisto/kallisto.merged.gene_tpm.tsv",
146+
"kallisto/kallisto.merged.transcript.SummarizedExperiment.rds",
147147
"kallisto/kallisto.merged.transcript_counts.tsv",
148148
"kallisto/kallisto.merged.transcript_lengths.tsv",
149149
"kallisto/kallisto.merged.transcript_tpm.tsv",

‎tests/min_mapped_reads.nf.test.snap‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -976,16 +976,16 @@
976976
"star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP1.seq.DupRate.xls",
977977
"star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.pos.DupRate.xls",
978978
"star_salmon/rseqc/read_duplication/xls/RAP1_UNINDUCED_REP2.seq.DupRate.xls",
979+
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
979980
"star_salmon/salmon.merged.gene_counts.tsv",
980981
"star_salmon/salmon.merged.gene_counts_length_scaled.tsv",
981982
"star_salmon/salmon.merged.gene_counts_scaled.tsv",
982983
"star_salmon/salmon.merged.gene_lengths.tsv",
983984
"star_salmon/salmon.merged.gene_tpm.tsv",
985+
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
984986
"star_salmon/salmon.merged.transcript_counts.tsv",
985987
"star_salmon/salmon.merged.transcript_lengths.tsv",
986988
"star_salmon/salmon.merged.transcript_tpm.tsv",
987-
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
988-
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
989989
"star_salmon/samtools_stats",
990990
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
991991
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",

‎tests/nofasta.nf.test.snap‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -324,8 +324,6 @@
324324
"salmon/WT_REP2/logs/salmon_quant.log",
325325
"salmon/WT_REP2/quant.genes.sf",
326326
"salmon/WT_REP2/quant.sf",
327-
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
328-
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
329327
"salmon/deseq2_qc",
330328
"salmon/deseq2_qc/R_sessionInfo.log",
331329
"salmon/deseq2_qc/deseq2.dds.RData",
@@ -339,11 +337,13 @@
339337
"salmon/deseq2_qc/size_factors/WT_REP1.txt",
340338
"salmon/deseq2_qc/size_factors/WT_REP2.txt",
341339
"salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
340+
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
342341
"salmon/salmon.merged.gene_counts.tsv",
343342
"salmon/salmon.merged.gene_counts_length_scaled.tsv",
344343
"salmon/salmon.merged.gene_counts_scaled.tsv",
345344
"salmon/salmon.merged.gene_lengths.tsv",
346345
"salmon/salmon.merged.gene_tpm.tsv",
346+
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
347347
"salmon/salmon.merged.transcript_counts.tsv",
348348
"salmon/salmon.merged.transcript_lengths.tsv",
349349
"salmon/salmon.merged.transcript_tpm.tsv",

‎tests/remove_ribo_rna.nf.test.snap‎

Lines changed: 4 additions & 4 deletions
Original file line numberDiff line numberDiff line change
@@ -612,8 +612,6 @@
612612
"salmon/WT_REP2/logs/salmon_quant.log",
613613
"salmon/WT_REP2/quant.genes.sf",
614614
"salmon/WT_REP2/quant.sf",
615-
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
616-
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
617615
"salmon/deseq2_qc",
618616
"salmon/deseq2_qc/R_sessionInfo.log",
619617
"salmon/deseq2_qc/deseq2.dds.RData",
@@ -627,11 +625,13 @@
627625
"salmon/deseq2_qc/size_factors/WT_REP1.txt",
628626
"salmon/deseq2_qc/size_factors/WT_REP2.txt",
629627
"salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
628+
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
630629
"salmon/salmon.merged.gene_counts.tsv",
631630
"salmon/salmon.merged.gene_counts_length_scaled.tsv",
632631
"salmon/salmon.merged.gene_counts_scaled.tsv",
633632
"salmon/salmon.merged.gene_lengths.tsv",
634633
"salmon/salmon.merged.gene_tpm.tsv",
634+
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
635635
"salmon/salmon.merged.transcript_counts.tsv",
636636
"salmon/salmon.merged.transcript_lengths.tsv",
637637
"salmon/salmon.merged.transcript_tpm.tsv",
@@ -1138,16 +1138,16 @@
11381138
"star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls",
11391139
"star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls",
11401140
"star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls",
1141+
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
11411142
"star_salmon/salmon.merged.gene_counts.tsv",
11421143
"star_salmon/salmon.merged.gene_counts_length_scaled.tsv",
11431144
"star_salmon/salmon.merged.gene_counts_scaled.tsv",
11441145
"star_salmon/salmon.merged.gene_lengths.tsv",
11451146
"star_salmon/salmon.merged.gene_tpm.tsv",
1147+
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
11461148
"star_salmon/salmon.merged.transcript_counts.tsv",
11471149
"star_salmon/salmon.merged.transcript_lengths.tsv",
11481150
"star_salmon/salmon.merged.transcript_tpm.tsv",
1149-
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
1150-
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
11511151
"star_salmon/samtools_stats",
11521152
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
11531153
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",

‎tests/salmon.nf.test.snap‎

Lines changed: 1 addition & 1 deletion
Original file line numberDiff line numberDiff line change
@@ -273,12 +273,12 @@
273273
"salmon/WT_REP2/quant.genes.sf",
274274
"salmon/WT_REP2/quant.sf",
275275
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
276-
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
277276
"salmon/salmon.merged.gene_counts.tsv",
278277
"salmon/salmon.merged.gene_counts_length_scaled.tsv",
279278
"salmon/salmon.merged.gene_counts_scaled.tsv",
280279
"salmon/salmon.merged.gene_lengths.tsv",
281280
"salmon/salmon.merged.gene_tpm.tsv",
281+
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
282282
"salmon/salmon.merged.transcript_counts.tsv",
283283
"salmon/salmon.merged.transcript_lengths.tsv",
284284
"salmon/salmon.merged.transcript_tpm.tsv",

‎tests/sentieon_default.nf.test.snap‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -1217,16 +1217,16 @@
12171217
"star_salmon/rseqc/read_duplication/xls/WT_REP1.seq.DupRate.xls",
12181218
"star_salmon/rseqc/read_duplication/xls/WT_REP2.pos.DupRate.xls",
12191219
"star_salmon/rseqc/read_duplication/xls/WT_REP2.seq.DupRate.xls",
1220+
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
12201221
"star_salmon/salmon.merged.gene_counts.tsv",
12211222
"star_salmon/salmon.merged.gene_counts_length_scaled.tsv",
12221223
"star_salmon/salmon.merged.gene_counts_scaled.tsv",
12231224
"star_salmon/salmon.merged.gene_lengths.tsv",
12241225
"star_salmon/salmon.merged.gene_tpm.tsv",
1226+
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
12251227
"star_salmon/salmon.merged.transcript_counts.tsv",
12261228
"star_salmon/salmon.merged.transcript_lengths.tsv",
12271229
"star_salmon/salmon.merged.transcript_tpm.tsv",
1228-
"star_salmon/salmon.merged.gene.SummarizedExperiment.rds",
1229-
"star_salmon/salmon.merged.transcript.SummarizedExperiment.rds",
12301230
"star_salmon/samtools_stats",
12311231
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.flagstat",
12321232
"star_salmon/samtools_stats/RAP1_IAA_30M_REP1.markdup.sorted.bam.idxstats",

‎tests/sentieon_star_rsem.nf.test.snap‎

Lines changed: 2 additions & 2 deletions
Original file line numberDiff line numberDiff line change
@@ -599,8 +599,6 @@
599599
"salmon/WT_REP2/logs/salmon_quant.log",
600600
"salmon/WT_REP2/quant.genes.sf",
601601
"salmon/WT_REP2/quant.sf",
602-
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
603-
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
604602
"salmon/deseq2_qc",
605603
"salmon/deseq2_qc/R_sessionInfo.log",
606604
"salmon/deseq2_qc/deseq2.dds.RData",
@@ -614,11 +612,13 @@
614612
"salmon/deseq2_qc/size_factors/WT_REP1.txt",
615613
"salmon/deseq2_qc/size_factors/WT_REP2.txt",
616614
"salmon/deseq2_qc/size_factors/deseq2.size_factors.RData",
615+
"salmon/salmon.merged.gene.SummarizedExperiment.rds",
617616
"salmon/salmon.merged.gene_counts.tsv",
618617
"salmon/salmon.merged.gene_counts_length_scaled.tsv",
619618
"salmon/salmon.merged.gene_counts_scaled.tsv",
620619
"salmon/salmon.merged.gene_lengths.tsv",
621620
"salmon/salmon.merged.gene_tpm.tsv",
621+
"salmon/salmon.merged.transcript.SummarizedExperiment.rds",
622622
"salmon/salmon.merged.transcript_counts.tsv",
623623
"salmon/salmon.merged.transcript_lengths.tsv",
624624
"salmon/salmon.merged.transcript_tpm.tsv",

0 commit comments

Comments
 (0)